[gmx-users] question about g_sas

[Dallas Warren]

>1. what is the unit of surface accessible area ? what
>does yaxis  label "Area (nm\S2\N)" mean? what are S2
>and N here?

nm^2 i.e. nanometers squared

\S means superscript and \N means end of line or return.  These are tags 
for one of the graphing problems that the data files are written to be read by.

>2. If I index a particular residue and calculate SAS
>for that residue, does program take the residue as a
>single residue in vacuo and calculates SAS or it
>calculates SAS only for those parts of the residue
>which are not buried and are actually exposed to
>solvent?

Not 100% sure how it actually does the calculation, but it takes a 0.14nm 
probe "molecule" (which is the default) and calculates the surface area of 
the surface it can move around the aggregate.  And this is of the atoms 
defined in the index group that you choose.  This will also include 
internal surfaces that may not contain any solvent, but there is sufficient 
space between neighbouring atoms to include the probe.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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